Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_BVLB-N1-BDNA-1_A23TY32LT4_1/1241_BVLB-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/e19cf12ae7bb74214c9a9a078d65ea/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/e19cf12ae7bb74214c9a9a078d65ea/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_BVLB-N1-BDNA-1_A23TY32LT4_1/1241_BVLB-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1241_BVLB-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BVLB-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BVLB-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1241_BVLB-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 104199999 total, 74649 skipped (flags/unmapped)
Fragments: 52262160 total (51809576 tlen-paired, 4732 hash-paired, 452 singletons, 21574 discordant, 425826 orphans, 13654 too large [>5000 bp], 21885786 duplicates)
Reads: 112840473 total, 68346 skipped (flags/unmapped)
Fragments: 56594347 total (56124271 tlen-paired, 6984 hash-paired, 533 singletons, 15377 discordant, 447182 orphans, 15574 too large [>5000 bp], 23370074 duplicates)
Reads: 112516081 total, 67931 skipped (flags/unmapped)
Fragments: 56439142 total (55923250 tlen-paired, 5622 hash-paired, 413 singletons, 19164 discordant, 490693 orphans, 30486 too large [>5000 bp], 23807704 duplicates)
Reads: 124545011 total, 125099 skipped (flags/unmapped)
Fragments: 62616806 total (61336992 tlen-paired, 6878 hash-paired, 464 singletons, 251734 discordant, 1020738 orphans, 103751 too large [>5000 bp], 26376603 duplicates)